Three-dimensional (3D) genome structure is crucial for the regulation of gene expression, with transcription factors playing irreplaceable roles in shaping genomic chromatin conformation. The transcription factor MAX is known to influence the proliferative fates of various cell types; however, the specific roles of MAX in the regulation of 3D genome remain underexplored. In this study, we performed an integrative analysis of MAX binding sites, gene expression, chromatin accessibility and interactions from porcine skeletal muscle satellite cells (PSCs) and mouse C2C12 cells to investigate the effect of MAX on the formation of the 3D genome. We found that the number of MAX binding sites decreased significantly with myoblast differentiation in both PSCs and C2C12 cells, which suggests an important role for MAX in the proliferative phase. Based on PolⅡ ChIA-PET data and Hi-C data, 83,403-124,428 polⅡ loops and 31145-39701 Hi-C loops (25kb) were identified in the proliferation and differentiation phases of PSCs and C2C12 cells. Classification of these loops indicated that 74.29% of them were enhancer-promoter (E-P) and enhancer-enhancer (E-E) interactions. Relative risk assessment analysis showed that the binding of MAX was strongly associated with loop formation during the proliferative phase but not during the differentiation phase in the two muscle cell types. Furthermore, DE genes between the proliferative and differentiation phase of muscle cells associated with MAX-binding loops were significantly enriched in Gene Ontology (GO) terms related to muscle contraction, muscle development, and the cell cycle. These findings illuminate the role of MAX in regulating the proliferation and differentiation of mammalian skeletal muscle satellite cells through the regulation of remote interactions mediated by Pol II, which provides new insights into the elucidation of mechanisms underlying meat yield traits in agricultural animals.

Skeletal muscle satellite cells, Transcription Factor, Chromatin loop, Transcription regulation